The augmentations would cost peanuts compared to the equipment operated.

I agree with this to an extent, but I think it would only apply to the targeting gunners on capital ships' spinal mounts, and maybe some bays on flagships. Turret gunners? No. (And player character gunners probably want to be turret gunners, because adventurers don't typically travel in ships with spinal weapons.)

Who's to say that people will want to be augmented? Not everyone is interested in having tech grafted, sometimes permanently, on to their bodies. Even if it does provide an advantage.

Players might, but that's why their are disadvantages socially to body augments on some worlds.

I think this would be a significant limiting factor on the use of augmentations. Although people in active military service would have access to specialized medical facilities that could work around augmentations, that's no longer true after they muster out. Do they come with permanent access to military hospitals?

Additionally, how long a commitment to serve does one need to make if they get an augmentation? How many gunners want to sign up for a bunch of extra years?

The augmentations is question as a package exceed a gunners projected salary by around 353 mos of pay, not really a good investment for the navy in bulk.

An alternate way of looking at this, if a gunner is allowed to keep his/her augments on mustering out, what fee can s/he command when out of the service and on the open market? Granted, you might argue the same as any other gunner with the same skill but how many would there be of that ability? As a PC, I can see some haggling going on, likewise for any former naval crew. Few if any free trader captains will pay for the augments but would be happy to take the benefits.

This is still secondary to my earlier post that the salaries need reviewing.

The problem would be the military not wanting to release the gunner for at least 20-30 years in order to justify the cost if it was given to a line crewman. ( That 20-30 year investment would make a buyout far more than the cost of the aug package.)

Let's assume that crew signs up for 4 year terms and serve on average 8 years (on board ship, training excluded). That means we have to replace each crew member every 8 years. Presumably we have more people than the absolute minimum, let's say we have two full crews for each ship. So, for every crew position we need to replace 2 people every 8 years or about 1/4 people every year.

Take a ship like this (from this thread): viewtopic.php?p=919571#p919571
It costs MCr ~4000 and has a crew of ~100 (including marines). By my assumptions we need to recruit and augment 100 / 4 ≈ 25 people every year.

A basic augmentation package (skill augmentation, a wafer jack, and some software) costs about MCr 0.065. Augmenting 25 people every year would cost 25 × 0.065 ≈ MCr 1.6 per year.

Operating a warship costs about 10% of the price per annum according to TCS. The ships also needs replacing occasionally. TCO would be about 15% of new price, or for my assumed ship MCr 4000 × 15% ≈ MCr 600 per year.

The basic augmentation package (for everyone including the assistant cook) would add MCr 1.6 to a budget of MCr 600 and add a +2 DM on most ship tasks. That is a complete no-brainer. I would charge you with dereliction of duty if you did not do it.

Characteristic augmentation is much more expensive. The TL12 characteristic +2 augmentation costs MCr 1. To augment the entire crew would cost 100 / 4 × 1 ≈ MCr 25 per year. To augment only the most critical roles (officers, bridge crew and gunners) would cost ~60 / 4 × 1 ≈ MCr 15 per year compared to a total budget of MCr 600 per year or about 2.5% more for an almost DM +1 on most tasks. Still worth it.

Which only work for Ortillery and Bays/Spinal weapons as wafer jacks only grant Int/Edu skills, screens and turrets are dex based tasks.

I thought so too, but was proven wrong...

A Traveller using an Expert package may make a skill check as if he had the skill at the software’s Bandwidth -1. Only INT and EDU-based checks can be attempted, however. If a Traveller already has the skill, then an Expert package will grant DM+1 to his check.

Yet also:

• A ship running an Intellect program and Expert Pilot can act as the pilot.

Core, p155. Piloting a ship is DEX based.

So it would seem that a person without skill can only attempt INT/EDU tasks, but Expert software can be used with all tasks for other purposes.

The consideration to take into account is the cost per person compared to the pay for each, with the basic package your stuffing 60,000 cr worth of gear into someone who is only paid 3,000 /mos.

To make matters worse, capital ships have 100s of gunners alone which aggravates the issue.

On the other hand, you can invest in a smaller pool of special operations naval section which would be more viable for augmentation as a whole and would require a lower duration to make cost effective. ( Also easier to justify release after service.)

A ship running an Intellect program and Expert Pilot can act as the pilot.

The Key is the intellect program which is a form of AI and would require access to the ships computer.

Which only work for Ortillery and Bays/Spinal weapons as wafer jacks only grant Int/Edu skills, screens and turrets are dex based tasks.

Nope - I said in the 3I, not MgT2e rules.

Wafer technology in T5, MWM's novel and therefore the 3I setting can be used for any skill. MgT2e has the rules for wafer jacks, but it doesn't have quite the same rules as T5 or the setting examples as per the novel.